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Protocols

GENCODE specifications

Information


Unique identifier OMICS_06416
Name GENCODE
Restrictions to use None
Community driven No
Data access File download, Browse, Application programming interface
User data submission Not allowed
Version 24.0
Maintained Yes

Taxon


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Maintainers


  • person_outline Paul Flicek
  • person_outline Adam Frankish

Publications for GENCODE

GENCODE citations

 (790)
library_books

Computational identification and validation of alternative splicing in ZSF1 rat RNA seq data, a preclinical model for type 2 diabetic nephropathy

2018
Sci Rep
PMCID: 5955895
PMID: 29769602
DOI: 10.1038/s41598-018-26035-x

[…] ated that the majority of mammalian genes can be alternatively spliced to generate multiple different isoforms that encode proteins with diverse, and even opposing, biological functions. In the human Gencode annotation Release 25, the number of annotated transcripts is more than three times the number of annotated genes; for protein coding genes, this ratio increases to 7:1. It has also been repor […]

call_split

Optimizing exosomal RNA isolation for RNA Seq analyses of archival sera specimens

2018
PLoS One
PMCID: 5940186
PMID: 29738525
DOI: 10.1371/journal.pone.0196913
call_split See protocol

[…] r than 20 bp. Trimmed reads were aligned to version hg38 of the human genome reference sequence using STAR []. Mapped reads were then matched to genomic features (i.e. mRNAs and lncRNAs) annotated in GENCODE25 [] and ERCC annotations using Rsubread package, version 1.24.0 [], to generate raw counts for each gene. Raw read count data were normalized to ERCC spike-in values across samples using Bioc […]

library_books

Time resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3

2018
BMC Biol
PMCID: 5937035
PMID: 29730990
DOI: 10.1186/s12915-018-0518-3

[…] FASTQ files were adapter- and quality-trimmed using Trim Galore!, and aligned with TopHat2 using hg19 genome index and GENCODE v19 transcriptome model. Alignment metrics and statistics were extracted from the BAM files using Picard tools. Reads were summarized to the GENCODE v19 genes with the summarizeOverlaps functi […]

library_books

Bidirectional promoters exhibit characteristic chromatin modification signature associated with transcription elongation in both sense and antisense directions

2018
BMC Genomics
PMCID: 5930751
PMID: 29716520
DOI: 10.1186/s12864-018-4697-7

[…] TSS of bidirectional genes is less than 1000 bp, 974 gene pairs were used for subsequent analysis. The location of the transcription start and end sites for each transcript were obtained from the VM9 GENCODE database. […]

library_books

The senescence associated secretory phenotype is potentiated by feedforward regulatory mechanisms involving Zscan4 and TAK1

2018
Nat Commun
PMCID: 5928226
PMID: 29712904
DOI: 10.1038/s41467-018-04010-4

[…] rophoresis. Arraystar Human LncRNA microarray v3.0 designed for global profiling of human LncRNAs (32,586) and protein-coding transcripts (26,109) covering all entries of Refseq, UCSC known genes and Gencode was employed. RNA labeling and array hybridization were performed according to a one-color microarray-based gene expression analysis protocol (Agilent) with minor modifications. Briefly, mRNA […]

call_split

A compendium of long non coding RNAs transcriptional fingerprint in multiple myeloma

2018
Sci Rep
PMCID: 5920050
PMID: 29700321
DOI: 10.1038/s41598-018-24701-8
call_split See protocol

[…] s not null. Quality Control (QC) analysis was performed using multiqc tool and the QC metrics were comparable for all samples. The annotation allowed to detect 14,202 lncRNAs, including the following Gencode biotypes: lincRNA, antisense, bidirectional promoter lncRNA, sense intronic, sense overlapping, 3′ overlapping ncRNA. The expression filter retained 9,540 lncRNAs in our dataset. […]

Citations

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GENCODE institution(s)
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA; Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland; Department of Medical Oncology, Inselspital, University Hospital, University of Bern, Bern, Switzerland; Department of Biomedical Research (DBMR), University of Bern, Bern, Switzerland; MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Department of Bioscience, Brunel University London, Uxbridge, UK; Functional Proteomics, Division of Cancer Biology, Institute of Cancer Research, London, UK; Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain; Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain; Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT, USA; Systems Biology Institute, Yale University, West Haven, CT, USA; Centre of New Technologies, University of Warsaw, Warsaw, Poland; Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA; Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, USA; Department of Computer Science, Yale University, New Haven, CT, USA; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Department of Medical and Molecular Genetics, King’s College London, Guys Hospital, Great Maze Pond, London, UK
GENCODE funding source(s)
Supported by National Human Genome Research Institute of the National Institutes of Health [U41HG007234]; Wellcome Trust [WT108749/Z/15/Z,WT200990/Z/16/Z]; European Molecular Biology Laboratory; Swiss National Science Foundation through the National Center of Competence in Research ‘RNA & Disease’ and Medical Faculty of the University of Bern.

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